We are studying the heterogeneity of inner dynein arm organization in Chlamydomonas flagella. Transverse and longitudinal thin sections have been cut and imaged in the CTEM. Image averaging techniques have been used to determine if a particular mutation results in a structural defect that is either specific or localized to a specific region of the flagellum. The structural differences have been correlated with the biochemical phenotype of a number of mutants using gel electrophoresis and fplc. From this work, we have detected at least one mutation that results in a structural defect that is characteristic of the dynein associated with only certain microtubule doublets. We are now using strains that have defects in phototaxis to identify differences in cis/trans flagella. Using existing programs and image processing techniques, we are examining the heterogeneity of inner dynein arm organization.